1XM8 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF GLYOXALASE II FROM ARABIDOPSIS THALIANA GENE AT2G31350

Authors :   G. E. Wesenberg, D. W. Smith, G. N. Phillips Jr. , E. Bitto, C. A. Bingman, S. T. M. Allard, Center For Eukaryotic Structural Genomics (Cesg)

Date :   01 Oct 04 (Deposition) - 12 Oct 04 (Release) - 19 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Structural Genomics, Protein Structure Initiative, Psi, Cesg, At2G31350, Metallo-Hydrolase, Zinc/Iron Binuclear Center, B-Lactamase Fold, Thioester Hydrolase, Mitochondrial Isozyme, Center For Eukaryotic Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. P. Marasinghe, I. M. Sander, B. Bennett, G. Periyannan, K. W. Yang, C. A. Makaroff, M. W. Crowder
Structural Studies On A Mitochondrial Glyoxalase Ii.
J. Biol. Chem. V. 280 40668 2005
PubMed-ID: 16227621 | Reference-DOI: 10.1074/JBC.M509748200
(for further references see the PDB file header)

Molecule 1 - GLYOXALASE II
	Chains	:	A, B
	EC Number	:	3.1.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGLX2-5/PT7-7
	Expression System Strain	:	BL21(DE3) ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AT2G31350
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	FE	2	Ligand/Ion	FE (III) ION
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	FE	-1	Ligand/Ion	FE (III) ION
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	FE	-1	Ligand/Ion	FE (III) ION
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:54 , HIS A:56 , HIS A:112 , ASP A:131 , FE A:701 , HOH A:901	BINDING SITE FOR RESIDUE ZN A 700
2	AC2	SOFTWARE	ASP A:58 , HIS A:59 , ASP A:131 , HIS A:169 , ZN A:700 , HOH A:901	BINDING SITE FOR RESIDUE FE A 701
3	AC3	SOFTWARE	HIS B:54 , HIS B:56 , HIS B:112 , ASP B:131 , FE B:704 , HOH B:802	BINDING SITE FOR RESIDUE ZN B 703
4	AC4	SOFTWARE	ASP B:58 , HIS B:59 , ASP B:131 , HIS B:169 , ZN B:703 , HOH B:802	BINDING SITE FOR RESIDUE FE B 704
5	AC5	SOFTWARE	PHE A:134 , SER A:137 , CYS A:138 , LYS A:140 , ARG A:248 , LYS A:251 , HOH A:1099	BINDING SITE FOR RESIDUE ACY A 800
6	AC6	SOFTWARE	LYS A:202 , HOH A:1113	BINDING SITE FOR RESIDUE PEG A 900
7	AC7	SOFTWARE	PHE B:134 , SER B:137 , CYS B:138 , LYS B:140 , ARG B:248 , LYS B:251 , HOH B:968	BINDING SITE FOR RESIDUE ACY B 801

(no "SS Bond" information available for 1XM8)

Asymmetric Unit

No.	Residues
1	Ile A:207	-	Pro A:208
2	Ile B:207	-	Pro B:208

(no "SAP(SNP)/Variant" information available for 1XM8)

(no "PROSITE Motif" information available for 1XM8)

(no "Exon" information available for 1XM8)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:254
 aligned with GLO2N_ARATH | Q9SID3 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:254
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320    
          GLO2N_ARATH    71 LQIELVPCLKDNYAYILHDEDTGTVGVVDPSEAEPIIDSLKRSGRNLTYILNTHHHYDHTGGNLELKDRYGAKVIGSAMDKDRIPGIDMALKDGDKWMFAGHEVHVMDTPGHTKGHISLYFPGSRAIFTGDTMFSLSCGKLFEGTPKQMLASLQKITSLPDDTSIYCGHEYTLSNSKFALSLEPNNEVLQSYAAHVAELRSKKLPTIPTTVKMEKACNPFLRSSNTDIRRALRIPEAADEAEALGIIRKAKDDF 324
               SCOP domains d1xm8a_ A: Glyoxalase II (hydroxyacylglutathione hydrolase)                                                                                                                                                                                                    SCOP domains
               CATH domains 1xm8A00 A:1-254 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeeeee......eeee...hhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhh.eeeee.hhhhhh..eeeee....eeee..eeeeeee........eeeeehhh.eeeee..ee..ee......hhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xm8 A   1 MQIELVPCLKDNYAYILHDEDTGTVGVVDPSEAEPIIDSLKRSGRNLTYILNTHHHYDHTGGNLELKDRYGAKVIGSAMDKDRIPGIDMALKDGDKWMFAGHEVHVMDTPGHTKGHISLYFPGSRAIFTGDTMFSLSCGKLFEGTPKQMLASLQKITSLPDDTSIYCGHEYTLSNSKFALSLEPNNEVLQSYAAHVAELRSKKLPTIPTTVKMEKACNPFLRSSNTDIRRALRIPEAADEAEALGIIRKAKDDF 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with GLO2N_ARATH | Q9SID3 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:254
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320    
          GLO2N_ARATH    71 LQIELVPCLKDNYAYILHDEDTGTVGVVDPSEAEPIIDSLKRSGRNLTYILNTHHHYDHTGGNLELKDRYGAKVIGSAMDKDRIPGIDMALKDGDKWMFAGHEVHVMDTPGHTKGHISLYFPGSRAIFTGDTMFSLSCGKLFEGTPKQMLASLQKITSLPDDTSIYCGHEYTLSNSKFALSLEPNNEVLQSYAAHVAELRSKKLPTIPTTVKMEKACNPFLRSSNTDIRRALRIPEAADEAEALGIIRKAKDDF 324
               SCOP domains d1xm8b_ B: Glyoxalase II (hydroxyacylglutathione hydrolase)                                                                                                                                                                                                    SCOP domains
               CATH domains 1xm8B00 B:1-254 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                CATH domains
           Pfam domains (1) ------Lactamase_B-1xm8B01 B:7-169                                                                                                                                        ------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------Lactamase_B-1xm8B02 B:7-169                                                                                                                                        ------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeee...eeeeeee......eeee...hhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhh.eeeee.hhh.....eeeee....eeee..eeeeeee........eeeeehhh.eeeee..ee..ee......hhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xm8 B   1 MQIELVPCLKDNYAYILHDEDTGTVGVVDPSEAEPIIDSLKRSGRNLTYILNTHHHYDHTGGNLELKDRYGAKVIGSAMDKDRIPGIDMALKDGDKWMFAGHEVHVMDTPGHTKGHISLYFPGSRAIFTGDTMFSLSCGKLFEGTPKQMLASLQKITSLPDDTSIYCGHEYTLSNSKFALSLEPNNEVLQSYAAHVAELRSKKLPTIPTTVKMEKACNPFLRSSNTDIRRALRIPEAADEAEALGIIRKAKDDF 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Metallo-beta-lactamase; Chain A (92)

Homologous Superfamily: Metallo-beta-lactamase, chain A (92)

Thale cress (Arabidopsis thaliana) (2)

1a	1xm8A00	A:1-254
1b	1xm8B00	B:1-254

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Metallo-HOrase (67)

Family: Lactamase_B (53)

Arabidopsis thaliana (Mouse-ear cress) (2)

1a	Lactamase_B-1xm8B01	B:7-169
1b	Lactamase_B-1xm8B02	B:7-169

Asymmetric Unit(hide GO term definitions)

Chain A,B (GLO2N_ARATH | Q9SID3)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004416	hydroxyacylglutathione hydrolase activity	Catalysis of the reaction: (S)-(2-hydroxyacyl)glutathione + H2O = glutathione + a 2-hydroxy carboxylate.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0019243	methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione	The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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	Cis Peptide Bonds
		Ile A:207 - Pro A:208	[ RasMol ]
		Ile B:207 - Pro B:208	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1XM8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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